That said, what if a lot of the questions in the system were little more than an erroneous misreading of the game’s finale moments – and that BioWare had actually delivered one of the most interesting, and downright ballsy, endings in video game history?

While some Mass Effect fans have likely heard of the “Indoctrination Theory” in passing over the last few weeks, a lot of players who have been busy expressing their outrage on BioWare forums, may have missed-out on an especially intriguing analysis of the, now, controversial endings – one that isn’t going to solve all their frustrations but might, just might, help convince them that BioWare actually tried to do something pretty special with the final chapter in Shepard’s trilogy.

From this point on we will be presenting MAJOR SPOILERS for Mass Effect 3 as well as the prior installments in the series. If you haven’t completed Mass Effect 3, and do not want to be spoiled, turn away now and come back when you’ve experienced the endings for yourself.

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Still here? As mentioned, the “Indoctrination Theory” has been gaining momentum over on the BioWare forums – ever since a few especially observant fans began to dissect the final fifteen minutes of the game (essentially everything that occurs after Shepard and company dash to the reaper beam). Over the last few weeks, as more and more gamers complete Mass Effect 3, other players have begun to contribute ideas, connections, and A/V content to the Indoctrination Theory community. The result is a pretty compelling alternate take on the Mass Effect 3 finale – a take that might explain why BioWare delivered an ending that was “unsatisfying” to so many people.

The Indoctrination Theory isn’t likely to provide gamers with a lot of the answers they’ve been seeking (such as what happened to all of their in-game friends) or remedy their frustration over the lack of “choices” in the game’s final moments; however, the theory would indicate that, not only is the ending much deeper (drawing from countless ideas presented earlier in the series), BioWare wasn’t actually being lazy with the ending, they were actively attempting to do something really ambitious.

At its core, the Indoctrination Theory asserts that, in the final moments of Mass Effect 3, Shepard is wrestling with reaper indoctrination and (in some variations of the theory) that he never actually makes it up to the Citadel at all. His final confrontation with the Illusive Man and his rendezvous with Anderson (as well as the Citadel AI) never actually happened – instead, the game presents a series of moments that showcase the degradation (or liberation) of Shepard’s mental state as the reapers attempt to fully-indoctrinate our main man.

The Indoctrination Theory thread at the BioWare forums is currently sitting at over 815 pages (and counting) – you can read the full posting HERE; however, we’ve included some of the more interesting tidbits below, including an amazing must-see video that lays-out all of the theory highlights as well as ties the Mass Effect 3 endings to events in prior installments with carefully selected footage and audio from Mass Effect, Mass Effect 2, and Mass Effect 3:

Here are a few of the main highlights from the theory thread (again, for the lengthy breakdown – head to the full BioWare forum post):

Shepard could have been indoctrinated on multiple occasions – through various interactions with Reaper-controlled characters and systems including Sovereign, the Mass Effect 2 “Human” Reaper, and “The Arrival” artifact.

No one but Shepard interacts with (or even notices) the Vancouver child – the one who appears in Shepard’s dreams and is revealed at the end of the game to be the Catalyst. The boy is merely an avatar used by the Reapers to manipulate, and ultimately indoctrinate, Shepard.

The final “choice” in the game is nothing more than manipulation by the Reapers in order to indoctrinate Shepard. Harbinger presents the three options in a way that plays-to Shepard’s emotions – to coerce him into letting the Reapers live.

If Shepard chooses Control, he essentially gives-in to Reaper control – since they are already, in part, controlling his mind. During his argument with “The Illusive Man,” Shepard made the exact same point – though Harbinger attempts to convince Shepard that he, unlike The Illusive Man, has the power to control the Reapers – which is, in the end, just a lie.

If Shepard chooses Synthesis, he opens the door for every organic in the galaxy to be infected with Reaper code – a process that was detailed earlier in the game by Legion with regard to the Geth indoctrination. Similar to Control, in this case, the Reapers successfully indoctrinate Shepard.

If Shepard chooses Destroy, he successfully resists indoctrination – though the overall outcome of the game (what happens to friends as well as the Reapers outside of Shepard’s head) is, ultimately, unclear. Unlike the other two scenarios, Shepard is shown waking-up (where as he’s fully-indoctrinated after either the Synthesis or Control options).

Note the reversal of Paragon and Renegade options when saving Anderson from being shot by The Illusive Man and at the end with the final “choice.”

Assuming the Indoctrination Theory is true, it certainly won’t get BioWare off the hook for the lack of side-character closure or the lack of multifaceted choices in the game’s closing moments. That said, compared with a surface-level interpretation of what is shown in the endings, it’s hard not to (at the very least) want to believe that BioWare didn’t slip-up, and instead delivered one of the most ambitious closing acts in gaming history – even if it went over a lot of heads. The Indoctrination take on the ending actually makes a lot of sense and could explain why the end was so unsatisfying to many gamers – since, if you’re taking it at face-value, a lot of the events are pretty underwhelming.

Players might not be faced with the choices they were expecting – but that’s because the choices in the end-game are exceptionally complicated – and, despite what it might seem, are rooted in a lot of subtle information that was delivered throughout the series’ three installments.

BioWare forum member “LookingGlassMind” puts it best:

“This moment, when you are standing there, agonizing over your choice? This is your indoctrination moment. This is where, it could be (fantastically and insanely) argued that this is the moment when indoctrination and all of its insidious power becomes as real as it possibly CAN be to the Player. Think about it! We stand there. We agonize. We freak out about the ridiculous choices, and we wonder (like Shepard would) why we just can’t ARGUE with the Catalyst (like Shepard would). And then, as this reality seems to be the only way forward (much like how indoctrination presents a version of reality to the indoctrinated that he/she sees as being the ONLY REAL OPTION – echoes of TIM, Kai Leng, Saren here), we begin to accept it. Tremulously, we start to make our choice.”

Ultimately, it’s unclear at this point whether or not the Indoctrination Theory outlines BioWare’s true intentions or is merely, as can be the case with subjective storytelling interpretation, an explanation that has been retrofitted onto an abstract and open-ended finale.

Even if the theory is spot-on, it’s equally unclear where the developers will take players next – given that an interesting ending doesn’t mean it’ll be satisfying to angry players. Even the “good” Indoctrination ending (achieved by destroying the reapers) concludes on a cliff-hanger with Shepard simply waking up – and does not address what happened to fan-favorite side-characters, among countless other issues that frustrated fans have pointed out.

While we’re certainly not endorsing the Indoctrination Theory as irrefutable, it’s worth sharing if for no other reason than to reflect on the end-game choice we each made – and whether or not, after considering this alternate take, we’d make that same choice again.

124 Comments

Ok i just want to express this. The catalyst said this ” he could not control us hecause we already controlled him.” meaning if he was indoctrinated then he couldnt have controlled the reapers

the prothean vi wouldve recognized the fact that he was indoctrinated when they met it on the temple on thessia. Instead he only mentioned indotrinated when keibleng came up to crash the party. Indoctrination is just a sorry way to try and rationalize the endings…face it the reapers are either controlled, destroyed or all life becomes mixed with organic and synthetic. These endings are what we are stuck with. Shepard was never indoctrinated. He was never onboard a reaper ship long enough to be indoctrinated. Otherwise all your squadmates are indoctrinated as well. Harbinger never got shepard bc lazarus cell got to him first and completely rebuilt him. So all this garbage where the final battle is going on is just stupid. It means the crucible wws simply a metal ball, game loses its meaning, and EA has lost even more respect

Just because you can fight back, doesn’t mean you aren’t indoctrinated. It takes tons of convincing, and specific dialoge choices to make him realize his mistake.

He’s at the point where the taint of indoctrination is obvious, but that doesn’t mean you can’t fight back.

Also, by the time Saren Reaches Vigil, Saren had been upgraded by the Reapers to try and make sure he doesn’t do what he did at the end, fight back. So if that isn’t completely obvious to anyone, much less the VI that he’s indoctrinated…

Also, yes they lost when the Reapers first invaded the Citadel. The point I was making, if you paid any attention to Mass Effect 3 (of which you clearly haven’t played) is that it is specifically stated that their were two factions of Protheans, one wanted to control, the other to destroy. The ones who wanted to control were indoctrinated, but they didn’t realize that until it was to late.

If their technology allowed for them to sense any sort of indoctriation, then they would have detected that the control people were being used. Yet it didn’t because obviously the taint wasn’t strong enough, at that point they really thought they were right…wow, just like the Illusive Man!

You telling me he isn’t indoctrinated? That at most points he truly didn’t believe in what he tried to accomplish?

Omg I think i finally understand the endings.
Ok so from the start of mass effect two, Cerberus get the remains of your body after Normandy blows up. Your brain dead at that point so the illusive man uses reaper tech to fire up your brain (making you think again.) The reaper tech however start to slowly corrupt you, Indoctrination you. After the alliance and the council ignores your warning about the reaper invasion, the corrupt process begins to spread, with thoughts that the Illusive man may have been right, while Anderson role suppresses that notion and gives you the hope.
The Child at the start represents the future, along with how you can’t save it, while Anderson states in the next scene that if we continue to fight and soldier on, we win will (hope).
The dreams are the Indoctrination process gaining a grip on your mind, once again showing you that you can’t save the future, its doomed to burn in ash, but your crew members and love interests, once again interfere to make sure the process can’t spread to quick.
After the red beam its you at the end of the game, the Indoctrination process speeds up, where you much choose between giving in to the Illusive man ideas, or siding with Anderson and stay on course. After getting rid of the Illusive man, you suddenly have defeated the process of Indoctrination, thus allowing you to take the next step.
The next step (The last part of the game) is actually you indoctrinating the Reapers. As the failed Indoctrination creates a bridge for you to travel into the reapers consciousness, much like the mission with the Geth, were you enter the Geth network to shut down a server.
The holographic child the creator of the reapers, using the child form to represent the future, who alerts you on the consequence of what will happen with your indoctrinating of the Reapers, by its calculations.
Red equals destroy: In which you will destroy the reapers, but in return will bring chaos and unrest to the galaxy,(Reapers were created to maintain order which is why it is red.)
Green equals mixing organics with reaper based code: meaning that synthetics and organs will share equality and DNA, most like what the Protheans had in mind many years ago, before their destruction.
Blue represents control of the reapers. You will be Indoctrinated by this choice, but you will control the reapers, as they know you to be a strong entity worthy to control them.
As I see it the reapers are not a selfish force bent on destruction, so much as a slave race, doing what they are designed to do. Many of the reapers look at Sheppard as a rather odd entity, a beacon of light and a small shred of hope, which may bring a change to the current way of old machine code which resides.

I got an understanding for this ending because as legion states in the Geth server mission, Sheppard as an infinity for guns,(You know and love guns like a typical gun nut.) you straight away notice it has infinite ammo and dosn’t overheat. The only other time you have a gun with infinite ammo is the geth server mission. So sheppard actually did make it to the white beam of light, which transferred him to the main reaper server. the reapers try to indoctrinate you, as a defense but fails. Then you are beamed up to the main server, the boy being yes from your dreams and also, the basic code that made the reapers. it knows you will indoctrinate change, it wants changes, it only warns you of the change you will make.

umm… not quite.
Project Lazarus didn’t use Reaper Tech. they didn’t have enough of it. it was just an extremely expensive application of technology we already had. and Shepard indoctrinating the Reapers? i don’t know where that came from. your last paragraph makes a lot of sense, but isn’t what the video is trying to explain; the last scene happens (supposedly) in Shepard’s mind.

Ok, so this all happene in his mind? Illusive man and anderson are still alive? so was he dead and never reached the white beam and the whole hallucnation in his mind happened as he was dying? since no one noticed he was alive whn he began walking towards the beam means that he was dying?

Is it possible that this all happened after the Collectors blew up the Normandy? The planet that they are on in the end scene is them going to look for Sheaperd? (Thinking outside the box)

Otherwise I think that this thepory makes the most sense, and it also sets it up perfectly for the DLC downloads. All of the stuff that we see in the end cutscene is in Sheaperds head except the breathing part at the end. Through this whole game you had to make choices about people living and dying, and if they died their spot was sually taken by someone else by a different name. I think the DLC will play off of him living, if you chose to destroy, to get up and try and beat the Reapers, and the others will be about you being someone on your crew (Ashley, Liara etc…) Looking for Sheaperd and eventually having to kill him to stop the attack.

At first I hated this ending, but now I am really excited to see what they bring in the DLC.

hate to say it but while this is a good explanition for about the last 15 min, if there is dlc to further the game ill be pissed. Masseffect was set up to be a trilligy it got a sucky ending and the ending dlc that hits this summer might clean up the ending or it might not, also looks like there setting up for more games. multi player is great but should have been made as a stand alone type game and more time spent on slingal player couse it is so riddled with bugs it not even funny. ME universe was fun to play in but look at all the other games that have gone beyound 3. prequeal tend to try to rewrite and sequals 4+ eather ignore imporant events or make them irrevelent. fighting game are the exception to this because they rarely include single player content and those that do tend not to stary from the lore behind the char.

If you go back and play the first game again-there’s a couple of interesting points that play into the entire theory. There are a lot of examples actually, but a couple hit me differently after playing ME3. In ME1-I was walking down the area where the ME relay “statue” or artwork is and the Avina is explaining it. When I was walking past it with Kaiden and Garrus-Kaiden uttered the same line that Vega does in Me3. “Do you hear that humming, or it is just me? It’s making my teeth tingle.” When I got to Virmire-and spoke with that Asari scientist, and she said that any contact with the Reaper will begin the subtle change of indoctrination, and you can hear it as humming, or a tingle. At the end, when you face Saren, depending on if you are renegade or paragon-Saren informs Sheppard, “I am the ultimate evolutionary future, this is where all of organic destiny lies-we are both machine and organic with the advantages of both, and the weaknesses of neither.” In ME3 Hackett tells you that the Illusive man is wrong, control of the Reaper is not the answer, dead Reapers are the answer. All three endings therefore, fit entirely with the story-because the instant that Sheppard was pulled in by that beacon on Eden Prime-that’s what started the indoctrination-and Hackett is right-the only way to end it-is to destroy the machines, once and for all-even Vigil said it on Illos, even it if means killing off the Geth, and all technology for generations. That’s why the Normandy had to land where it did-it’s the new Garden of Eden-with organic lives, unless you pick to control or synthesis with the Reapers-it couldn’t end any other way. The only way the Reapers lose-is if you choose to kill them off completely. If you go back now and re-play the games-all the way up and pay attention to all the comments and have as many conversations as you can, well it’s damned interesting and a much more intricate story than I think a lot of people are capable of understanding.
Of course..maybe I’m indoctrinated now as well.

ME3 is the only Mass Effect game that I played, but I did find a pattern in ME3’s plot that, if you pay attention, will help you know which path to take at the end. First, when the salarians and turians put the genophage machine on Tuchanka to maintain “order” over the krogan, you had the option of destroying the machine or siding with the salarians. Destroying the machine saved the krogan, which eventually helped preserve Palaven. If you sided with the Salarians, the krogan would slowly die off under the machine’s power. My other example is the situation at the end of the quarian and geth war. If you sided with the non-organic geth, the organic quarians would have no hope and would eventually be wiped out. If you sided with the quarians, the synthetic geth would be destroyed and an entire race of organics would stat to thrive. The geth were initially made to maintain order for the quarians. So, throughout the campaign, the game portrayed the destroying of machines made to preserve order as the factor that saved entire species of organic life. That describes the destroying of the Reapers pretty well.

Just got a bump from this site to check this article, never have seen that before.

OK, my first take on IT is that it was an attempt of the gamers to understand how ME3 could be considered an ending. Given the abrupt change from being able to reason in conversations, and being able to argue, to being forced to agree, just because the little boy says so, was a big step to make, and most people seemed to fall off the cliff if they missed it.

But now that I have read the fully fleshed out theory I still disagree. IT is not viable, and does not fit the conversations or anything else that happens at the end of ME3. The actual answer is a matter of scale, and one lone puny human just happened to be in the right place, like the cliché goes, and for once you got to observe the butterfly wings that brought the wind of change to the galaxy. Subtle? Yeah, really subtle, but still there, and easy to spot as well. You can argue, but the Catalyst has responses that invalidate your arguments, and remove the discussion from the realm of “you are doing something bad, I’m here to make you stop” and into the realm of “I want to change the cosmos, what options do I have” Considering there are FOUR choices available, Control, Destroy, Synthesize or Refuse (my first choice was refuse, it was hard to make) they give you all the insight you need to understand the scope of your dilemma.

Anyway, it was a awesome ending, with an incredible backdrop, and an incredible change from the insane battle to a lonely conversation on a enigmatic space station with an AI that has incomplete species interaction programming due to a race of beings that over-estimated their understanding of the universe. Leviathan stands as a warning against technical pride, same as the old Terminator movies.

The very simple reason this isn’t the truth is because Bioware didn’t say anything. Consider it. Bioware came under immense attack from fans over the ending. They could have ended all of that in an instant by saying he was indoctrinated, you just missed the hints. But they didn’t, because that’s not what happened.

Don’t get me wrong, I do like this idea. I feel it would have needed a little more clarity if this was canon, like the last shot of Shepard’s face showing him indoctrinated, or something. It can’t just hang there like a cobbled together piece of theory that it still is.

But again, I go back to my main point. during all these years since the release, Bioware never said this was the ending. Even when people came up with the theory, they could have jumped in and said yes! We were waiting for someone to figure it out. They didn’t. And for that simple reason I can never consider this the actual ending